FlexStationFormatToCSV

Converts a Molecular Devices FlexStation 3 Microplate Reader .csv file to an easier-to-use format.

---

Overview

Certain instruments like the Microplate Reader output in block CSV format where each plate data is in a separate block (See Example Below). This script converts that block-based (horizontal) layout into a flat CSV format that is easier to analyze in spreadsheets, scripts, or downstream pipelines.

Example input block format (from FlexStation)

Plate: Row13_DMI_t0 1.3
Temperature(C),A1
24.5,-0.004283333
24.5,-0.002208333
~End
Plate: Row13_QoI_t0 1.3
Temperature(C),A1
24.5,0.1707
24.5,0.1259

Converted output format (flat CSV)

Example (5-column layout):

Sample,TimePoint,Well,Coordinate,Absorbance
1,0,A1,0,-0.022333333
2,0,A2,0,-0.031166667

Column headers:

Sample, TimePoint, Well, Coordinate, Absorbance

---

Usage

Command line

cat "your_file".csv | FlexStationFormatToCSV.py > "output".csv

If you use the wildcard *, you can run it on multiple files at once.

Example (multiple files)

cat *.csv | FlexStationFormatToCSV.py > combined_output.csv

---

Files

• FlexStationFormatToCSV.py — conversion script
• test_file.csv — expected input format example
• test_output.csv — expected output format example

---

Expected Formats

Expected input format in test_file.csv

The input should follow the FlexStation block layout, where each plate appears in its own section and ends with ~End.

Expected output format in test_output.csv

The output should be a normalized CSV with one row per sample/well measurement.

---

Why did I make this? Why not?

• Block-based output isn't fun to work with
• This script allows the user to go from block-based instrument exports to tabular CSV data
• Makes downstream analysis easier in Python/R/Excel
• Simplifies batch processing of multiple files